He was wounded at the Second Battle of Fort Fisher by a musket ball to his leg, and died in prison camp on March 10, 1865, of dysentery.

Appointed second lieutenant of engineers, Whiting was involved in constructing seacoast defenses in Maryland and Florida, and surveying military routes and frontier forts in West Texas.

Promoted to first lieutenant in 1853, Whiting was sent west, erecting harbor fortifications in San Francisco, California, and serving on the board of engineers for Pacific Coast defenses until 1856.

On January 3, Whiting received information that Georgia was moving to take Fort Marion, but he made no effort to warn the garrison there or its commander.

By the end of the month, more than half a dozen U.S. Army forts, arsenals, and barracks had fallen to state forces without any action by Whiting.

[2] Later, Whiting served under General Joseph E. Johnston as chief engineer of the Army of the Shenandoah and at the First Battle of Bull Run.

On December 19, Whiting sent a letter to President Jefferson Davis declining his assignment to command five fresh Mississippi regiments, and instead gave unsolicited advice and criticism to his superiors.

The division comprised the commands of several brigadier generals who would distinguish themselves over the course of the war, notably John Bell Hood, Wade Hampton III, and Evander Law, as well as Colonel Dorsey Pender.

On the Confederate withdrawal from Yorktown to Richmond, Whiting's men were responsible for blocking a Union flanking maneuver by sea, at the Battle of Eltham's Landing.

Finally promoted to major general on February 13, 1863, Whiting was assigned command of the Department of North Carolina and Southern Virginia, briefly taking over the Petersburg defenses in May 1864.